Application of Recurrence Plot Analysis to Examine Dynamics of Biological Molecules on the Example of Aggregation of Seed Mucilage Components.

The goal of the research is to describe the aggregation process inside the mucilage produced by plant seeds using molecular dynamics (MD) combined with time series algorithmic analysis based on the recurrence plots. The studied biological molecules model is seed mucilage composed of three main polysaccharides, i.e. pectins, hemicellulose, and cellulose. The modeling of biological molecules is based on the assumption that a classical-quantum passage underlies the aggregation process in the mucilage, resulting from non-covalent interactions, as they affect the macroscopic properties of the system. The applied recurrence plot approach is an important tool for time series analysis and data mining dedicated to analyzing time series data originating from complex, chaotic systems. In the current research, we demonstrated that advanced algorithmic analysis of seed mucilage data can reveal some features of the dynamics of the system, namely temperature-dependent regions with different dynamics of increments of a number of hydrogen bonds and regions of stable oscillation of increments of a number of hydrophobic-polar interactions. Henceforth, we pave the path for automatic data-mining methods for the analysis of biological molecules with the intermediate step of the application of recurrence plot analysis, as the generalization of recurrence plot applications to other (biological molecules) datasets is straightforward.

Characterization of Synovial Fluid Components: Albumin-Chondroitin Sulfate Interactions Seen through Molecular Dynamics.

The friction coefficient of articular cartilage (AC) is very low. A method of producing tailor-made materials with even similar lubrication properties is still a challenge. The physicochemical reasons for such excellent lubrication properties of AC are still not fully explained; however, a crucial factor seems to be synergy between synovial fluid (SF) components. As a stepping stone to being able to produce innovative materials characterized by a very low friction coefficient, we studied the interactions between two important components of SF: human serum albumin (HSA) and chondroitin sulfate (CS). The molecular dynamics method, preceded by docking, is used in the study. Interactions of HSA with two types of CS (IV and VI), with the addition of three types of ions often found in physiological solutions: Ca2+, Na+, and Mg2+, are compared. It was found that there were differences in the energy of binding values and interaction maps between CS-4 and CS-6 complexes. HSA:CS-4 complexes were bound stronger than in the case of HSA:CS-6 because more interactions were formed across all types of interactions except one-the only difference was for ionic bridges, which were more often found in HSA:CS-6 complexes. RMSD and RMSF indicated that complexes HSA:CS-4 behave much more stably than HSA:CS-6. The type of ions added to the solution was also very important and changed the interaction map. However, the biggest difference was caused by the addition of Ca2+ ions which were prone to form ionic bridges.

Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface.

Albumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions on human serum albumin-hyaluronan/chondroitin-6-sulfate interactions examined using molecular docking followed by molecular dynamics simulations. We analyze chosen glycosaminoglycans binding by employing a conformational entropy approach. In addition, several protein-polymer complexes have been studied to check how the binding site and presence of ions influence affinity. The presence of divalent cations contributes to the decrease of conformational entropy near carboxyl and sulfate groups. This observation can indicate the higher affinity between glycosaminoglycans and albumin. Moreover, domains IIIA and IIIB of albumin have the highest affinity as those are two domains that show a positive net charge that allows for binding with negatively charged glycosaminoglycans. Finally, in discussion, we suggest some research path to find particular features that would carry information about the dynamics of the particular type of polymers or ions.

Matter-Aggregating Low-Dimensional Nanostructures at the Edge of the Classical vs. Quantum Realm.

This commentary tackles the subtle at-the-edge problem of passing locally by a mesoscopic matter-aggregating system from a classical stochastic to a quantum stochastic description. A d-dimensional entropy-productive aggregation of the matter is taken as the starting point. Then, a dimensional reduction towards a one-dimensional quantum-wire type matter-aggregation system is proposed, resulting in postponing surface-tension conditions for the effectively d = 1-dimensional quantum-wire type or nanorod-like cluster/polycrystal, which is qualitatively consistent with a physical-metallurgical (high-temperature) Louat's grain growth model. A certain recuperative interplay based on maneuvering between subtle temperature rises applied to the system under study while maintaining its quantum character (the so-called Nelson's quantum-stochastic procedure) within the limits of a vanishing Planck's constant, involved in the diffusivity measure of the aggregation, is discussed. Certain applications towards the formation of d = 1-dimensional semiconductors and other nanostructures (possibly using soft materials or (bio)polymeric materials such as nanofibers) are envisioned. As a special example, one may propose a nanotechnological process which is termed the Van der Waals heteroepitaxy. The process itself contains the main quantum vs. classical crossover due to the involvement of weak repulsion (quantum) vs. attraction (treated classically) interactions, which are represented by a Lennard-Jones-type potential.

Interactions between Beta-2-Glycoprotein-1 and Phospholipid Bilayer-A Molecular Dynamic Study.

This study aims to investigate the interactions appearing when the beta-2-glycoprotein-1 binds to a lipid bilayer. The inter- and intra-molecular forces acting between the two macromolecular systems have been investigated using a molecular dynamics simulation method. The importance of water bridges has also been addressed. Additionally, the viscoelastic response of the bilayer has been studied. In detail, the (saturated-chain) 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and (unsaturated-chain) 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) bilayers have been chosen to test their behavior near the protein. Both of the lipids have a polar head but different chemical structures and are similar to the main phospholipids present in the synovial fluid. This study is meaningful for further explaining the worsening friction properties in articular cartilage, as the inactivation of phospholipid bilayers by beta-2-glycoprotein-1 is believed to be a cause of the destruction of cartilage in most rheumatic diseases and osteoarthritis. It was found that the protein binds stronger to the DPPC bilayer than to the POPE, but in both cases, it has the potential to change the local bilayer stability. Nevertheless, the binding forces are placed within a small area (only a few lipids contribute to the binding, creating many interactions). However, together, they are not stronger than the covalent bonds between C-O, thus, potentially, it is possible to push the lipids into the bilayer but detaching the lipids' heads from the tail is not possible. Additionally, the protein causes water displacement from the vicinity of the bilayer, and this may be a contributor to the instability of the bilayer (disrupting the water bridges needed for the stabilization of the bilayer, especially in the case of DPPC where the heads are not so well stabilized by H-bonds as they are in POPE). Moreover, it was found that the diffusivity of lipids in the DPPC bilayer bound to the protein is significantly different from the diffusivity of the ones which are not in contact with the protein. The POPE bilayer is stiffer due to intramolecular interactions, which are stronger than in the DPPC; thus, the viscous to elastic effects in the POPE case are more significant than in the case of the DPPC. It is, therefore, harder to destabilize the POPE bilayer than the DPPC one.

[Systematic review and meta-analysis of epidemiology, prophylaxis and therapy of infections with viral hepatitis B and C in Polish paediatric oncology centres]. / Przeglad systematyczny i meta-analiza epidemiologii, profilaktyki i terapii zakazen wirusami zapalenina watroby typu B i C w Polskich osrodkach onkologii dzieciecej.

OBJECTIVE: Summary of published data on epidemiology, prophylaxis and therapy of HBV and HCV infections in Polish paediatric oncology centres. METHODS: Metaanalysis of available data from 1985-2008. RESULTS: 1. Epidemiology of HBV/HCV infections in 2070 patients. HBV infections in 716/1735 (41.3%), HCV in 497/1557 (31.9%), dual HBV+HCV in 76/707 (10.7%) patients. 2. Documented vaccinations against HBV infections before introduction of neonate vaccination in 1995 were carried out in 1056 children. In 614/985 (62.3%) patients seroconversion was detected, but 62/792 (7.8%) patients became infected. 3. Therapy with interferon was introduced in 188 patients; 89 with HBV, 41 with HCV and 58 with HBV+HCV. Response to interferon therapy defined as inhibition or decrease of viral replication or elimination of viral markers was documented in 37/188 (19.6%) patients. Alanine transaminase normalization occurred in 127/168 (75.6%) patients. 4. Protective effect against HBV infection after neonates/infants vaccination in 1995 was analyzed in 392 patients. Protective effect was obtained in 339/392 (86.5%) children, while infection with HBV occurred in 28/392 (7.1%) patients. During this period HCV infection was detected in 1/159 patients. No dual infections were found. CONCLUSIONS: Introduction of active immunoprophylaxis against HBV infections in haematology/oncology wards in 1989-1992, has led to 10-fold (p<0.00001), decrease of risk of HBV infection, and obligatory vaccination of infants/neonates in l995 additionally decreased the risk by 4-fold (p<0.00001). After introducing all prophylaxis measures, the risk of HBV infection decreased 38-fold (p<0.00001). Vaccination of neonates/infants has decreased 8-fold (p<0.00001), the risk of lack of anti-HBV. The risk of HCV infection decreased 74-fold (p<0.00001) in the same period. No risk of dual HBV+HCV infections was found currently.

On the protein crystal formation as an interface-controlled process with prototype ion-channeling effect.

A superdiffusive random-walk action in the depletion zone around a growing protein crystal is considered. It stands for a dynamic boundary condition of the growth process and competes steadily with a quasistatic, curvature-involving (thermodynamic) free boundary condition, both of them contributing to interpret the (mainly late-stage) growth process in terms of a prototype ion-channeling effect. An overall diffusion function contains quantitative signatures of both boundary conditions mentioned and indicates whether the new phase grows as an orderly phase or a converse scenario occurs. This situation can be treated in a quite versatile way both numerically and analytically, within a generalized Smoluchowski framework. This study can help in (1) elucidating some dynamic puzzles of a complex crystal formation vs biomolecular aggregation, also those concerning ion-channel formation, and (2) seeing how ion-channel-type dynamics of non-Markovian nature may set properly the pace of model (dis)ordered protein aggregation.